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ask again: disaster

@ I sent this help letter before but no response.I hope some one could help me out of trouble.

@ I am I do not know how to get the alignment file even  after i read through the tutorial. It seems that if you have a   @ template (preferred PDB code) and target seqeunce, and the alignment file in PIR format, you could  run homology @ modeling. Am  I  rignt ?

@ If i know the sequence of targets and template , what should i do next ?

*# Homology modelling by the MODELLER TOP routine 'model'.

*INCLUDE                                              # Include the predefined TOP routines (like c languange include <math.h>)

*SET OUTPUT_CONTROL = 1 1 1 1 1       # uncomment to produce a large log file
*SET ALNFILE  = 'alignment.ali'          # alignment filename   (where the pre-aligned file, "alignment.ali" come *from?)
*SET KNOWNS   = '5fd1'                     # codes of the templates
*SET SEQUENCE = '1fdx'                        # code of the target
*SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files
*SET STARTING_MODEL= 1                # index of the first model 
*SET ENDING_MODEL  = 1                # index of the last model
*                                                            # (determines how many models to calculate)

*CALL ROUTINE = 'model'              # do homology modelling